Billy:
Everything Steve said is true. But let me offer some alternatives.
For some reason it's not letting me see profiles, so I don't know what you've got for a boat, or even judge whether you want "high brow" or "low brow" activities.
DiMillo's is the former. A very well-protected marina with a nice restaurant right there. Both the restaurant and marina charge a premium for their location, and while good, are not great. But you are right in the center of everything on the Portland waterfront, from fine dining to fishermen's bars. Moving down the food chain, you have Portland Yacht Services. Much cheaper, but not as classy a marina. Plus it's not as well protected, so you might roll a little. But it's still a short walk to town, and even closer to the brewery, a bakery, even a narrow gauge railroad with museum. Hamilton Marine (a must-see) is just around the corner. And you could still call a cab if you want to explore beyond the waterfront.
If you're going to take a cab anyway, you might also look at Spring Point Marina, a very nice, well-protected marina, and they have fuel. But there's not much within walking distance except parks, lighthouses, oil terminals, etc. I think there is one restaurant there that's at least equal to DiMillos, but I forget if that's right at the marina, or a short walk away.
Another option is spending the night on Peaks Island. The marina there has slips (sometimes) and moorings for either overnight or day trips. Again you might roll some in the chop. Spending the night gives you the same access to all the shops and restaurants on the island as the day trippers, but you get a feel for island living - the ferry schedule sets the pulse of the island, and time your activities by the coming and going of the mobs of tourists.
I tried Great Diamond. Apparently we'd just missed George Bush Sr, who dined there the night before. We didn't feel the least bit welcome. After tying up for the night, we were read a long list of things we weren't allowed to do and places we weren't allowed to go. All the guides talk about old forts and walking trails. Forget it. You're restricted to one road. No trails. The usable government structures have been converted to condos or clubs or whatever, and the rest are off-limits. The island is privately owned and VERY exclusive. The residents paid a lot to own vacation homes there, and don't want to share. We respect that. We asked for our money back and left.
Freeport is a good destination, but you can take the boat there, too. Both slips and moorings are available, but you will need to take a cab to town unless you're a serious walker/hiker. Of course "town" means LL Bean, a must-see if you haven't been there. Last time I was there food was available, I think it was a fried seafood take-out, right at the marina.
You asked about Kennebunkport and Portsmouth. Of the two, I'd lean toward Portsmouth. K'port is OK, very skinny water and not much more welcoming than Great Diamond. Not much there for transients, IMHO.
Portsmouth Harbor is my home port, so I never get the opportunity to be a transient there. Again starting high on the social ladder, Wentworth Marina is the absolute best North of Newport RI. Golf, fine dining, a bar on the dock, and all the amenities of a fine resort (run by Marriott). And a price tag to match. The only possible down side is it's pretty isolated, nothing else to do outside the resort, but of course the concierge can arrange a cab into Portsmouth if that's a problem for you.
On the other end of the scale are two good options. You can anchor or take a mooring in Pepperell Cove on the Maine side, and there is a nice restaurant and old time country store, but not much else there, except great views of the mouth of the river. The cove is surprisingly well protected and quiet at night.
Upriver there's the Prescott Park docks. Very inexpensive, and right in the center of town. During the summer you can watch the play in the park from your boat, or take deck chairs up and enjoy it close up. You're minutes from a dozen restaurants, from the fine dining to the best taco stand around. Portsmouth is a great "little city" for just walking around, shopping, eating, brew pubs, whatever. The down side here is that there's no shoreside facilities like heads or showers, and you'll be bounced around by the wakes of all the charter and commercial fishing boats. It'll settle down at night, but the lobstermen start out early. If you want more amenities you can go just upriver to Harbor Place marina, where all the larger yachts stay. Still right in downtown, but it's a little more private, there are marina facilites, and for some reason the wakes aren't quite so bad.
If it's snotty outside, you can do an inland cruise to Great Bay. There isn't much to do there, but it's a scenic trip. You can anchor or (I didn't tell you this) find a mooring that no-one is using. For some reason, NH doesn't do very well at assigning moorings to people who actually USE them. Many sit unused for years, or even get handed down generation to generation. You take your chances though, some are better maintained than others.
The great cruising only starts at Casco Bay. But I think your plan is fine, don't overdue it your first time. You WILL want to come to Maine again, and each trip further down east will be an adventure. Plus there are lots of other good stops on your way up, Boston, Salem, etc.
